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WIP: ingest-to-phylo workflow
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joverlee521 committed Mar 26, 2024
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53 changes: 53 additions & 0 deletions .github/workflows/ingest-to-phylogenetic.yaml
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name: Ingest to phylogenetic

on:
workflow_dispatch:

jobs:
ingest:
permissions:
id-token: write
uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master
secrets: inherit
with:
# Starting with the default docker runtime
# We can migrate to AWS Batch when/if we need to for more resources or if
# the job runs longer than the GH Action limit of 6 hours.
runtime: docker
run: |
nextstrain build \
--env AWS_ACCESS_KEY_ID \
--env AWS_SECRET_ACCESS_KEY \
ingest \
--configfile build-configs/nextstrain-automation/config.yaml
# Specifying artifact name to differentiate ingest build outputs from
# the phylogenetic build outputs
artifact-name: ingest-build-output
artifact-paths: |
ingest/results/
ingest/benchmarks/
ingest/logs/
ingest/.snakemake/log/
# TKTK check for new data from ingest
# This can potentially interface with GH and/or S3?
# 1. Check last automated run's GH artifact output and diff with current S3 files
# 2. Check S3's previous version of outputs and diff with current S3 files

# TKTK phylo workflow
# Just realized the phylo workflow does not have automated build uploads

# phylogenetic:
# needs: [ingest]
# permissions:
# id-token: write
# uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master
# secrets: inherit
# with:
# runtime: docker
# run: |
# nextstrain build \
# --env AWS_ACCESS_KEY_ID \
# --env AWS_SECRET_ACCESS_KEY \
# phylogenetic \
# --configfile build-configs/nextstrain-automation/config.yaml

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